[RNABuilder-help] Re: pdb write bug in MMB 2.11

[Samuel Flores]

On Mar 7, 2013, at 11:45 PM, Michael Kuiper wrote:

> Greetings Samuel!
> 
> Please feel free to use any movies I send you any way you like.  I hope to have some more later. 
> 
> I think I've found a bug in 2.11 with regards to writing out large pdb files.  (I'm not quite sure the official way to report this) 
> 

I'm not sure i like how the fora work .. so for now writing to rnatoolbox-help at simtk.org is best

> It seems to me that if there are more than 100000 atoms, we will see a shift in the x,y,z coordinates due to the limitations in the  
> pdb format in the atom number column.   I've written a small python script that corrects these errors for myself but it is easier to do it in the source! 


If your molecules are big you should just see a reduction in the precision.  Can you send me your commands.dat and input structure file?

> 
> The error means that the large molecule trajectories are not displayed properly in vmd and also restarting from a 
> 'last.x.pdb' file also seems corrupted. 
> 
> For large atom numbers I use hexadecimal notation in pdb files. 
> 
> Have to run to a meeting,  
> chat soon! 
> 
> Mike
>